Fig 1.
General pedigree chart of X. tropicalis strains.
Frogs facing left represent the Ivory Coast strain and those facing right are Nigerian strains. Frogs colored black indicate strains used in this study. The arrows and figures next to frogs indicate transportation of animals and the years when those were held (if there is a record).
Fig 2.
Alignment of physical and genetic linkage maps of X. tropicalis.
Left = FISH cytogenetic map [16]. Middle = physical map from full nucleotide sequence data (JGI X. tropicalis genome assembly 7.1). Right = genetic map based on linkage analysis [12]. The sixty loci used in our analyses are indicated on the right. All maps are size proportional. Physical nucleotide units are mega base (Mbp), and genetic map units are centimorgan (cM).
Table 1.
Basic genotypic data of 60 SSLP markers in eleven X. tropicalis colonies.
Abbreviations: P, proportion of polymofic loci; NA, number of alleles; HE, expected heterozygosity; F, fixation index (i.e., inbreeding coefficient).
Fig 3.
Observed distribution of pairwise r estimates among X. tropicalis strains.
Box plots represent the distribution of relatedness values (r) of each strain. Mean and SD values are described in the parentheses below the labels.
Table 2.
Pairwise DA (below the diagonal) and Dps (above the diagonal) distances among X. tropicalis colonies.
Fig 4.
Neighbor joining trees and comparison of the control region structures of mitochondrial genomes.
(A) Neighbor joining trees of the strains based on genetic distances (DA) of SSLP data (left) and p-distance of mitochondrial haplotypes (2,328 nucleotide sites) (right). Numbers on branches indicate percent bootstrap probability (>50%). The values for SSLP tree are given in order for DA/DPS. (B) Comparison of the control region structures of mitochondrial genomes. Structures of the control region and alignments of identified putative origin of H-strand replication (OH), conserved sequence blocks (CSB-1-3), and repeat motifs are shown. (C) Neighbor joining tree of the strains and wild individuals based on p-distance of mitochondrial haplotypes (1,109 nucleotide sites).
Fig 5.
Plot of expected heterozygosity (HE) against generation number (t).
The curved dotted strain indicates theoretical reduction of heterozygosity via single brother-sister matings for every generation, calculated from the following equation: , where H0 is the heterozygosity of the founder colony, and Ne is effective population size (i.e., number of individuals that contribute to breeding). HE of F0 of N (Gurdon Inst.) (0.509) and 2 are used for H0 and Ne, respectively. Open rectangles indicate mean HE estimated from individual based simulation using VORTEX version 10 [43]. During simulation, allele frequencies of N (Gurdon Inst.) were used as initial allele frequency, and single brother-sister mating was conducted in every generation. The simulation was repeated one hundred times. Bar indicates standard deviation.